NCCAT Tomography Short Course
April 12-14, 2021
SEMC and NCCAT will be offering a 3-day workshop focused on the theory and practice of tomographic methods. Cryoelectron tomography (cryoET) is a powerful new method for directly visualizing macromolecular associations and organization in native cells Traditionally, macromolecular structure determination has been limited to the analysis of isolated molecules and structures. CryoET has the unique ability to visualize macromolecular organization in native cells; it utilizes the intrinsic contrast of frozen cellular material to directly image macromolecules.
Short Course Agenda
April 12, 2021
Day 1: Lectures and Roundtables
recordings: [Day 1 first half][Day 2 second half]
| 12:00-12:05 | Welcome |
| 12:05-12:50 | Lecture 1 – Intro and overview of ET Wei Dai (Rutgers University) [pdf of slides] |
| 12:50-13:35 | Lecture 2 – FIB-SEM Bill Rice (New York University) [pdf of slides] |
| 13:35-14:20 | Roundtable 1 – Making windows into cells & Choosing the right in situ target and model system |
| 14:20-14:45 | Break |
| 14:45-15:30 | Lecture 3 – Cryo-Applications and sub-tomogram averaging Alex Noble (NYSBC/SEMC) [pdf of slides] |
| 15:30-16:15 | Lecture 4 – Automated reconstruction, subtomogram averaging methods & data interpretation Steven Ludtke (Baylor College of Medicine) [pdf of slides] |
| 16:15-17:00 | Roundtable 2 – The future of in situ cellular structural biology |
| 17:00-17:30 | Closing and networking/break out rooms |
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April 13, 2021
Day 2: Practical – Appion Protomo (limited space available)
| 11:00-11:45 | Practical pre-requisite – Computational setup for workshop [AWS startup pdf] |
| 11:45-12:00 | Break |
| 12:00-12:05 | Welcome |
| 12:05-13:00 | Roundtable 3 – Introductions and flash talks by short course attendees [Flash talk speaker list][Flash talk slide deck pdf] recording: [Flash talks] |
| 13:00-17:00 | Practical 1 Appion III : Fiducial-less Tomography Practical Alex Noble (NYSBC/SEMC) [tutorial information] recording: [Appion-protomo & Dynamo] |
| 13:00-13:30 Full Overview – Tilt-Series Collection, Appion-Protomo alignment, and Sub-tomogram Processing 13:30-14:00 In-Depth Appion-Protomo Workflow 14:00-14:30 Q&A and Practice! 14:30-15:00 Discussion/Break 15:00-15:10 Overview – Sub-Tomogram Alignment and Dynamo 15:10-15:35 Particle Picking using a Template 15:35-16:00 Membrane, and Filament Picking 16:00-16:30 Sub-Tomogram Alignment, Classification, and tools to transfer to Warp/M/Relion 16:30-17:00 Q&A and Practice! 17:00 End |
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April 14, 2021
Day 3: Practical – EMAN2 (limited space available)
| 11:00-11:45 | Practical pre-requisite – Computational setup for workshop [AWS startup pdf] |
| 11:45-12:00 | Break |
| 12:00-12:05 | Welcome |
| 12:05-16:45 | Practical 2 EMAN2 tools, sub-tomogram averaging and annotation Muyuan Chen (Baylor College of Medicine) [tutorial information] recording: [EMAN2] |
| 12:05-12:50 Basic user interface and visualization of raw data. 12:50-13:35 Tilt series alignment, tomogram reconstruction and CTF estimation 13:35-14:30 Methods for picking particles from tomograms 14:30-15:00 Break 15:00-16:15 Generating initial model and setting up subtomogram averaging runs 16:15-16:45 Q&A |
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| 16:45-17:00 | Closing & Wrap up |
*All times ET.
